Protein crosslinks: Difference between revisions
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====Isopeptide Bonds==== | ====Isopeptide Bonds==== | ||
[[Isopeptide bonds]] are less common, but an estimate of their frequency may not be available. A text search for "isopeptide" at RCSB.Org gives ~400 hits, | [[Isopeptide bonds]] are less common, but an estimate of their frequency may not be available. | ||
*A text search for "isopeptide" at RCSB.Org gives ~400 hits (July, 2021). | |||
*A text search at PDBe gives ~12,000 hits (July, 2021). In a small sample of the latter hits, none contained the term "isopeptide". Also based on a small sample, some entries that contain verified isopeptide bonds do not contain the term (for example, [[5jqf]]). | |||
*Example: Bacterial pilus adhesin [[2xi9]] has 2 isopeptide bonds (and 2 thioester bonds). | *Example: Bacterial pilus adhesin [[2xi9]] has 2 isopeptide bonds (and 2 thioester bonds). | ||
Revision as of 20:53, 2 July 2021
Proteins are linear (unbranched) polypeptide chains of amino acids. The subject of this article is covalent crosslinks between polypeptides, either between protein chains (interchain crosslinks), or within chains (intrachain crosslinks).
Natural CrosslinksNatural Crosslinks
These crosslinks are formed either spontaneously during protein folding, or as a result of natural enzymatic processes.
Disulfide BondsDisulfide Bonds
Disulfide bonds are the most common protein crosslinks. About 23% of protein structures in the PDB have disulfide bonds (July, 2021[1]).
- Example: Insulin 9ins has 2 interchain and one intrachain disulfide bonds.
- Visualization: View 9ins in FirstGlance. In FirstGlance, in the Tools Tab, click Disulfides/S/Se.
Isopeptide BondsIsopeptide Bonds
Isopeptide bonds are less common, but an estimate of their frequency may not be available.
- A text search for "isopeptide" at RCSB.Org gives ~400 hits (July, 2021).
- A text search at PDBe gives ~12,000 hits (July, 2021). In a small sample of the latter hits, none contained the term "isopeptide". Also based on a small sample, some entries that contain verified isopeptide bonds do not contain the term (for example, 5jqf).
- Example: Bacterial pilus adhesin 2xi9 has 2 isopeptide bonds (and 2 thioester bonds).
- Visualization: View 2xi9 in FirstGlance. If you see "➤➤Show more details" in the Molecule Information Tab, click on that.
Thioester BondsThioester Bonds
Thioester bonds: Again, an estimate of frequency may not be available.
- A text search for "thioester" at RCSB.Org gives ~2,000 hits.
- A text search at PDBe gives ~1,400 hits (July, 2021). Among a sample of 5 of the PDBe hits (the first of every 100 in a listing sorted with best resolution at the top), none had thioester bonds, but most contained terms such as "thioesterase" or "thioester".
- Adding "and not thioesterase" to the PDBe search reduced the hits to ~500. Five hits were tested (the first of every 100 in a listing sorted with best resolution at the top) but none had thioester bonds.
- Example: Bacterial pilus adhesin 2xi9 has 2 thioester bonds (and 2 isopeptide bonds). Additional examples will be found in the lower left panel of FirstGlance when this example is viewed.
- Visualization: View 2xi9 in FirstGlance. If you see "➤➤Show more details" in the Molecule Information Tab, click on that.
Artificial CrosslinksArtificial Crosslinks
NotesNotes
- ↑ In July, 2021, the PDB had ~180,000 entries. Advanced search at RCSB.Org for "Polymer molecuar features: polymer entity type = protein" and "Deposited entry features: Disulfide bond count per deposited model > 0" gave ~41,000 hits, or about 23%.